National Surveillance of Antimicrobial Resistanceslmicrobiology.lk/download/National Surveillance of Antimicrobial Resistance 10Dec2014...National Surveillance of Antimicrobial Resistance:

National Surveillance of Antimicrobial Resistance

Report to Ministry of Health

by

Sri Lanka College of Microbiologists

SLCM ARSP & NLBSA Technical Committees

December 2014

National Surveillance of Antimicrobial Resistance: SLCM Report to MOH

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National Surveillance of Antimicrobial Resistance:

Report to Ministry of Health by SLCM

Background

Currently, national surveillance on antimicrobial resistance is carried out as two projects by the

Sri Lanka College of Microbiologists. The Antibiotic Resistance Surveillance Project (ARSP) which

produces data from blood culture isolates was started by the SLCM in a few selected hospitals

in 2009 and was expanded to all hospitals with consultant microbiologists by 2013. The parallel

project National Laboratory Based Surveillance of Antimicrobial Resistance of significant urine

culture isolates (NLBSA) was started following a meeting held in 2011 in the Ministry of Health,

with participation of the Director General of Health Services, the DDG/LS, Director (LS), Director

(MT&S) and many microbiologists from the hospitals and universities of Sri Lanka. Together,

these two projects enable us to gain a broader understanding of the extent of antimicrobial

resistance in Sri Lanka.

Implementation plan

Both projects were initiated under the guidance of Steering Committees and a Technical

Committee. The Technical Committee designed the way forward in implementing the activity.

Decisions were taken on

1) Scope of the activity

2) Data collection & distribution system

3) Needs assessment on fulfilling and sustaining the activity

Scope of the activity and data collection

ARSP

In 2009, at the initiation of ARSP, collecting data which is comparable and is of international

standard was difficult due to the non-availability of culture identification systems and the

uniformity of antibiotic resistance testing. To overcome these difficulties, the scope of the

activities included introducing identification of blood culture isolates to the species level,

supplying the essential antibiotic discs, streamlining the supply chain of the Ministry of Health

to provide the necessary items to sustain the project and introducing CLSI antibiotic sensitivity

testing method in all participant laboratories.


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In the first phase of the project, data on all Gram-negative culture isolates were entered into a

tailor made software. A few workshops were conducted by SLCM to train the microbiologists,

medical officers (where available) and the technical staff of microbiology laboratories to carry

out the project. Data dissemination was planned through scientific presentations and

publications.

NLBSA

As the initial step in surveillance of antimicrobial resistance in organisms causing UTI, the data

on isolates of midstream urine specimens with a colony count of ≥ 105 CFU/ml, was to be

entered into WHONET microbiology software in all hospitals with consultant microbiologists

and in microbiology departments of medical faculties with diagnostic laboratories. A few

workshops were planned and conducted by SLCM to train the microbiologists, medical officers

(where available) and technical staff of microbiology laboratories, in order to familiarize them

with using WHONET. It was planned to distribute the generated data through the website of

SLCM and by oral/poster presentations in the scientific sessions.

Needs assessment

A needs assessment was carried out by the SLCM among the expected participant institutes, in

order to find out the facilities available and the difficulties that may be encountered. This

revealed that many stations had difficulty in entering data due to shortage of manpower and

the non-availability of computers.

This issue was discussed with the DDG/LS of the Ministry of Health and a request was made for

data entry operators for the laboratories. Although the Ministry of Health does not have cadre

provision for data entry operators, a decision was taken to seek support from the heads of

institutions to obtain computers and to strengthen human resources in the microbiology

laboratories of all hospitals together with Consultant Microbiologists. The DGHS facilitated this

by allocating a time slot to the SLCM to discuss this at the regular MoH Directors’ meeting.

Progress to date

Following analysis of the needs assessment, the Technical Committee understood the

constraints in carrying out the proposed activity but decided to move forward nevertheless

because of its importance. While continuing the efforts to strengthen facilities in all

microbiology laboratories, it was decided to initiate activities in those institutions where the

minimum required facilities were already available.


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ARSP

The data of the first phase was analyzed and published in the Ceylon Medical Journal in 2013,

(See Annex 2 for copy of paper). This data has been used by the WHO in preparation of the

AMR report of South East Asia. The 1st phase was followed by the 2nd phase, which started in

2013 with all blood culture isolates. The available data of year 2013 is under analysis now.

NLBSA

For surveillance of AMR on UTI, only the Microbiology laboratories at the Lady Ridgeway

Hospital, Colombo North Teaching Hospital, Ragama, Sri Jayawardenapura General Hospital,

Nugegoda, BH Angoda (IDH), Peradeniya Teaching Hospital, Faculty of Medicine, Colombo

Faculty of Medicine, Ragama and GH Ratnapura were able to commence data entry.

In mid-2014, the SLCM decided to analyze the available data for 2013, and disseminate the

results by presentation at the Annual Scientific Sessions of the Sri Lanka College of

Microbiologists in September 2014 (See Annex 1 for copy of abstract).

The data was analyzed only in totality and is not age-group specific or disease-entity specific.

The susceptibility rates were calculated using the antibiogram reported to clinicians by the

laboratories.

Summary findings

Blood culture isolates

A total of 599 blood culture isolates were analyzed for the year 2013 (115 from paediatric

cases, 484 from adults). 138/599 isolates were from Intensive Care Units. Gram-negative

organisms were responsible for 61% of the infections with E. coli and Kleb. pneumoniae being

the commonest. Among Gram-positives, S. aureus (49%), S. pneumonia (13%), Group B

streptococci (10%), Enterococci (9%), and viridans streptococci (6%) were found. Common

organisms in ICUs included S. aureus, Acinetobacter, E. coli and Klebsiella. Of the Salmonella

isolates, 36% was S. paratyphi while 30% was S. typhi.

The rate of resistance in Acinetobacter isolates was very high, with 38% showing resistance to

cefeperazone salbactam. Among the isolates of S. aureus, 53% were MRSA. 95% of S.

pneumoniae isolates were penicillin resistant by disc diffusion method. 20% of E. coli isolates

and 28% of Klebsiella isolates were ESBL producers. They exhibited carbapenem resistance as


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well (E. coli 5-9%, Klebsiella 28-36%). 40% of Salmonella typhi and paratyphi isolates were

resistant to ciprofloxacin while 100% of isolates were susceptible to ceftriaxone.

Urinary isolates

The results from a total of 1175 significant isolates from four centres (Lady Ridgeway Hospital,

Sri Jayawardenepura General Hospital, Faculty of Medicine, Colombo and Faculty of Medicine,

Ragama) were analysed. As shown in Table 1, the large majority (n=922, 78.5%) were Gram-

negative enteric organisms, commonly known as coliforms. The other causative organisms are

as shown in Table 1.

Table 1. Significant isolates from urinary samples

Organism causing UTI Number of isolates Percentage

Coliforms 922 78.5%

Enterococcus spp 83 7.0%

Candida spp 60 5.1%

Pseudomonas spp 38 3.2%

Acinetobacter spp 21 1.8%

Gp B β-haemolytic streptococci 20 1.7%

Coagulase-negative staphylococci 10 0.9%

Streptococcus spp 9 0.8%

Staphylococcus aureus 7 0.6%

Staphylococcus saprophyticus 5 0.4%

Total isolates 1,175 100.0%

Table 2 shows the number of coliforms tested for antibiotic sensitivity by disc diffusion in the

analysed data. None of the 13 isolates of Acinetobacter species tested were sensitive to

meropenem while only 55% (16/29) of Pseudomonas spp. were sensitive to meropenem. 74%

(60/81) of Enterococcus species were sensitive to ampicillin.


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Table 2. Antibiotic sensitivity of coliform organisms

Antibiotic Number of isolates

tested

Number of sensitive

isolates

Percentage of

sensitive isolates

Meropenem 718 665 92.6%

Nirofurantoin 873 621 71.1%

Gentamicin 855 601 70.3%

Cefotaxime 883 422 47.8%

Cefuroxime 853 392 46.0%

Amoxicillin-clavulanic acid 819 341 41.6%

Ciprofloxacin 829 318 38.4%

Nalidixic acid 866 255 29.4%

Cephalexin 862 223 25.9%

Ampicillin 795 92 11.6%

Conclusions and recommendations

Severe infections with blood stream involvement (sepsis / bacteraemias) are caused by both

Gram-negative and -positive organisms. Acinetobacter, a highly resistant organism with few

antibiotic treatment options, is responsible for 1/5th of Gram-negative sepsis observed in ICUs.

ESBL production is common in E. coli and Klebsiella which require therapy with carbapenems in

most instances. Carbapenem resistance too has emerged in Gram-negatives.

The common occurrence of MRSA (53%) and ciprofloxacin-resistant Salmonella (40%) in typhoid

fever, in blood culture isolates should be strongly considered in empiric therapy.

The large majority of UTIs are caused by coliform organisms. The data from four centres

revealed a high resistance rate in coliforms against broad spectrum antibiotics like cefotaxime

and ciprofloxacin; 7.4% of the coliforms were resistant to meropenem. Acinetobacter sp.

showed a very high resistance rate even for carbapenems.

The results suggest that nitrofurantoin can still be used for empiric therapy for cystitis and

lower urinary tract infections, while ampicillin can be used as empirical therapy to treat UTI due

to enterococcus species. However, given that about 1/4th of coliforms are not sensitive to

nitrofurantoin, it is strongly recommended that the final choice of anti-microbial agent is based

on the results of urine culture and ABST.

It should also be noted that these analyses did not include data on patient age. The data

included in the analysis in both projects represented the major hospitals where antimicrobial


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resistance is naturally common. These two limiting factors should be taken into consideration

whenever the above information is used for patient management.

Important points to note and lessons learnt

Generating data pertaining to antibiotic resistance in the country is an important

component in the process of developing rational use of antibiotics. Rational use of

antibiotics has the potential to enormously reduce the health budget spent on

antibiotics. This has been highlighted by WHO and the Health Ministers of the WHO

South East Asia Region who have signed the Jaipur Declaration on AMR.

Up to now the SLCM has produced data on antibiotic sensitivity patterns in blood

culture isolates (through ARSP) and in urinary tract infections (through NLBSA), giving

information on serious systemic blood stream infections and UTIs. These data reflect the

current trends of antimicrobial resistance, and the organisms involved.

The available data suggest that antibiotic resistance is alarmingly frequent, and

highlights the importance of good antibiotic stewardship.

Data analysis has been restricted to a few centres so far because many others found

data entry difficult due to lack of computers and necessary manpower.

Generation of accurate national data which can be compared with international data

requires strong support from technical experts. Analysis of data available should be

done very sensibly to pick the presence of world trends in antibiotic resistance in the

country and the existing resistant mechanisms.

However without a continuous supply chain and without the necessary human

resources in laboratories, it is not possible to generate data that is truly representative

of the entire country. Therefore strengthening the microbiology laboratories to enable

generation of accurate, truly national data, is essential.

Support required for the future from the Ministry of Health

Strengthening microbiology laboratories in hospitals is a prime requirement to have a quality

output. Further improvement, especially with regard to generation of national data, will be

difficult within the existing work platforms. Therefore the following issues are highlighted for

necessary corrective action.

1. Large hospitals find data entry difficult due to problems associated with work load, even

though they are provided with computer facilities. Some of the larger hospitals still have


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very poor infrastructure with no computer facilities. On the other hand, some smaller

hospitals have all the required facilities, but quality output is not possible as the required

expertise is not available. All these issues hinder generation of high quality national data.

Therefore it is suggested that laboratories should be developed in phases, in an organized

fashion, paying particular attention to quality assurance. This will automatically lead to a

good data generation which will represent the whole country. The Sri Lanka College of

Microbiologists will be happy to provide the MoH with any technical inputs that may be

necessary for this purpose.

2. Continuous supply of culture media and antibiotic discs are primary requirements to

generate quality output from microbiology laboratories. Frequent interruption of supplies

greatly disrupts the generation of high quality data.

Therefore it is suggested to streamline and strengthen the existing supply chain to meet the

minimum requirement of the laboratories.

3. Training of technical staff with a view to improving their quality of work is essential in

generating reliable data. Although it may be said that the MOH is trying to achieve this

target, the training received by technical staff is neither well-targeted nor oriented towards

reaching the goals.

Therefore it is suggested to streamline and strengthen the existing system of training given

to technical staff, identifying the final target very clearly. Here again the SLCM is willing to

support the MoH in identifying appropriate targets and conduct training, etc.

4. A National Antibiotic Policy is essential in order to promote the rational use of antibiotics.

We suggest the formulation of a national antibiotic policy with participation of all relevant

sectors such as Ministry of Health, Ministry of Livestock, Sri Lanka College of Microbiologists,

Sri Lanka College of Physicians etc. This should be followed by development of an

implementation plan and a monitoring system. The active support of the SLMC will always

be there for this activity. Re-activating the National Alliance for Anti-Microbial Resistance

(AMR) in the Ministry of Health, Sri Lanka would also be helpful to carry out this task.


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Annex 1. Abstract presented at SLCM Sessions 2014

Documents

National Surveillance of Antimicrobial Resistanceslmicrobiology.lk/download/National Surveillance of Antimicrobial Resistance 10Dec2014...National Surveillance of Antimicrobial Resistance: